DNA samples taken from the body matched that of Yoo, 73, who owned Chonghaejin Marine, the operator of ferry Sewol, which capsized and sank off the southwestern coast April 16.
The body was discovered 40 days ago in the plum field some 2 km away from a vacation home where Yoo was believed was residing in May.
The body was found lying face up, wearing a winter jumper jacket, black pants and a hat. It was badly decomposed due to heavy rains and high humidity, police said. Beside the body, a couple of alcohol bottles were scattered around.
Body has been confirmed as that of Yoo Byung-eon
Police first believed that it was the body of a homeless person due to its shabby appearance.
There was no sign of foul play, but the exact cause of the death is still under investigation.
The accident, one of the country's worst, killed 294 people, mostly high school students with 10 people still missing.
Yoo and his family have been suspected of committing a host of illegal acts such as embezzlement, dereliction of duty and tax evasion, which led to lack of funds in the ferry operator.A massive manhunt was launched after the ferry disaster as Yoo and his family dismissed prosecutors' summons several times and ran away.
Arrest warrants were issued for Yoo's second son and eldest daughter, who are staying abroad, and Yoo and his eldest son have been placed on the most wanted list.
Prosecutors had offered a bounty of 500 million ($490,000) for Yoo, the highest amount in the country's history.
Yoo's wife and his 75-year-old elder brother as well as many assistants who are suspected of helping Yoo of fleeing has been arrested.